1
|
Hanna FE, Hunter CA. Polarisation effects on the H-bond acceptor properties of sulfonamides. Chem Commun (Camb) 2024. [PMID: 39319689 DOI: 10.1039/d4cc03530e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
The strengths of H-bonding interactions in networks are affected by cooperativity between the interacting sites. Compounds with an intramolecular H-bond between a sulfonamide NH group and pyridine nitrogen were used to measure the magnitude of cooperative effects on intermolecular H-bonding interactions with the sulfonamide oxygen. X-ray crystallography and 1H NMR experiments confirm the presence of the intramolecular H-bond and show that it is maintained in the 1 : 1 complex formed with perfluoro-tert-butanol (PFTB) in n-octane solution. Association constants for formation of 1 : 1 complexes with PFTB were determined using UV/Vis absorption titrations for a series of compounds equipped with different pyridine groups. Substituents on the pyridine were used to tune the strength of the intramolecular H-bond and investigate the effects on the strength of the intermolecular H-bond. Electron-donating groups on the pyridine that increase the strength of the intramolecular H-bond were found to increase in the strength of the intermolecular interaction with PFTB. The results were used to determine the H-bond acceptor parameters, β, for the sulfonamide oxygen group, and the values show a linear relationship with the value of β for the pyridine nitrogen. The slope of this relationship corresponds to the cooperativity parameter, κ, which is +0.16. The positive cooperativity observed in H-bonded sulfonamides is comparable to the value measured previously for the amide group (κ = +0.20).
Collapse
Affiliation(s)
- Fergal E Hanna
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| |
Collapse
|
2
|
Hanna FE, Root AJ, Schade M, Hunter CA. Negative cooperativity in the formation of H-bond networks involving primary anilines. Chem Sci 2024; 15:12036-12041. [PMID: 39092127 PMCID: PMC11290332 DOI: 10.1039/d4sc03719g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
Networks of H-bonds can show non-additive behaviour, where the strength of one interaction perturbs another. The magnitude of such cooperative effects can be quantified by measuring the effect of the presence of an intramolecular H-bond at one site on a molecule on the association constant for formation of an intermolecular H-bond at another site. This approach has been used to quantify the cooperativity associated with the interaction of a primary amine with two H-bond acceptors. A series of compounds that have an intramolecular H-bond between an aniline NH2 group and a pyridine nitrogen were prepared, using polarising substituents on the pyridine ring to vary the strength of the intramolecular H-bond. The presence of the intramolecular interaction was confirmed by X-ray crystallography in the solid state and NMR spectroscopy in n-octane solution. UV-vis absorption titrations were used to measure the association constants for formation of an intermolecular H-bond with tri-n-butyl phosphine oxide in n-octane. Electron-donating substituents on the pyridine ring, which increase the strength of the intramolecular H-bond, were found to decrease the strength of the intermolecular H-bond between the aniline and the phosphine oxide. The results were used to determine the H-bond donor parameters for the anilines, α, and there is a linear relationship between the values of α and the H-bond acceptor parameter of the pyridine group involved in the intramolecular H-bond, β. The slope of this relationship was used to determine the cooperativity parameter (κ = -0.10), which quantifies the negative allosteric cooperativity between the two H-bonding interactions. Calculated molecular electrostatic potential surfaces of the anilines quantitatively reproduce the experimental result, which suggests that effects are electrostatic in origin, either due to polarisation of the NH bonds or due to secondary electrostatic interactions between the two H-bond acceptors.
Collapse
Affiliation(s)
- Fergal E Hanna
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Alexander J Root
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Markus Schade
- Chemistry, Oncology R&D, AstraZeneca 1 Francis Crick Avenue Cambridge CB2 0AA UK
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| |
Collapse
|
3
|
Zhang J, Kriebel CN, Wan Z, Shi M, Glaubitz C, He X. Automated Fragmentation Quantum Mechanical Calculation of 15N and 13C Chemical Shifts in a Membrane Protein. J Chem Theory Comput 2023; 19:7405-7422. [PMID: 37788419 DOI: 10.1021/acs.jctc.3c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
In this work, we developed an accurate and cost-effective automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method to calculate the chemical shifts of 15N and 13C of membrane proteins. The convergence of the AF-QM/MM method was tested using Krokinobacter eikastus rhodopsin 2 as a test case. When the distance threshold of the QM region is equal to or larger than 4.0 Å, the results of the AF-QM/MM calculations are close to convergence. In addition, the effects of selected density functionals, basis sets, and local chemical environment of target atoms on the chemical shift calculations were systematically investigated. Our results demonstrate that the predicted chemical shifts are more accurate when important environmental factors including cross-protomer interactions, lipid molecules, and solvent molecules are taken into consideration, especially for the 15N chemical shift prediction. Furthermore, with the presence of sodium ions in the environment, the chemical shift of residues, retinal, and retinal Schiff base are affected, which is consistent with the results of the solid-state nuclear magnetic resonance (NMR) experiment. Upon comparing the performance of various density functionals (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB95, and OPBE), the results show that mPW1PW91 is a suitable functional for the 15N and 13C chemical shift prediction of the membrane proteins. Meanwhile, we find that the improved accuracy of the 13Cβ chemical shift calculations can be achieved by the employment of the triple-ζ basis set. However, the employment of the triple-ζ basis set does not improve the accuracy of the 15N and 13Cα chemical shift calculations nor does the addition of a diffuse function improve the overall prediction accuracy of the chemical shifts. Our study also underscores that the AF-QM/MM method has significant advantages in predicting the chemical shifts of key ligands and nonstandard residues in membrane proteins than most widely used empirical models; therefore, it could be an accurate computational tool for chemical shift calculations on various types of biological systems.
Collapse
Affiliation(s)
- Jinhuan Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Clara Nassrin Kriebel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Zheng Wan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
| |
Collapse
|
4
|
Hanna FE, Root AJ, Hunter CA. Polarisation effects on the H-bond acceptor properties of secondary amides. Chem Sci 2023; 14:11151-11157. [PMID: 37860643 PMCID: PMC10583693 DOI: 10.1039/d3sc03823h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/24/2023] [Indexed: 10/21/2023] Open
Abstract
H-bonding interactions in networks are stabilised by cooperativity, but the relationship between the chemical structures of the interacting functional groups and the thermodynamic consequences is not well-understood. We have used compounds with an intramolecular H-bond between a pyridine H-bond acceptor and an amide NH group to quantify cooperative effects on the H-bond acceptor properties of the amide carbonyl group. 1H NMR experiments in n-octane confirm the presence of the intramolecular H-bond and show that this interaction is intact in the 1 : 1 complex formed with perfluoro-tert-butanol (PFTB). UV-vis absorption titrations were used to measure the relationship between the association constant for formation of this complex and the H-bond acceptor properties of the pyridine involved in the intramolecular H-bond. Electron-donating substituents on the pyridine increase the strength of the intermolecular H-bond between PFTB and the amide. There is a linear relationship between the H-bond acceptor parameter β measured for the amide carbonyl group and the H-bond acceptor parameter for the pyridine. The cooperativity parameter κ determined from this relationship is 0.2, i.e. β for an amide carbonyl group is increased by one fifth of the value of β of an acceptor that interacts with the NH group. This result is reproduced by DFT calculations of H-bond parameters for the individual molecules in the gas phase, which implies that the observed cooperativity can be understood as polarisation of the electron density in the amide π-system in response to formation of a H-bond. The cooperativity parameter κ measured for the secondary amide H-bond donor and H-bond acceptor is identical, which implies that polarisation of an amide mediates the interaction between an external donor or acceptor in a reciprocal manner.
Collapse
Affiliation(s)
- Fergal E Hanna
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Alexander J Root
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| |
Collapse
|
5
|
Oliveira MP, Hünenberger PH. Force fields optimized against experimental data for large compound families using CombiFF: Validation considering non-target properties and polyfunctional compounds. J Mol Graph Model 2023; 118:108312. [PMID: 36252318 DOI: 10.1016/j.jmgm.2022.108312] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/09/2022] [Accepted: 08/16/2022] [Indexed: 10/14/2022]
Abstract
The CombiFF scheme is a workflow for the automated calibration of force-field parameters against condensed-phase experimental data considering simultaneously entire classes of organic molecules. The main steps of this scheme are: (i) selection of a molecule family; (ii) enumeration of all isomers; (iii) query for experimental data; (iv) automatic construction of the molecular topologies; (v) iterative refinement of the force-field parameters considering the entire family. In two recent articles, CombiFF was applied to the design of GROMOS-compatible united-atom force fields for the saturated acyclic haloalkanes and for saturated acyclic compounds involving eight common chemical functional groups of oxygen and nitrogen. This calibration and the subsequent initial validation involved two limitations: (i) the experimental data considered was restricted to values for the pure-liquid density ρliq and the vaporization enthalpy ΔHvap of the compounds; (ii) beyond monofunctional compounds, the training set only involved homo-polyhaloalkanes (possibly mixing halogen types) in the first study, and homo-polyfunctional compounds of the considered oxygen or nitrogen functional groups (no mixing of different group types) in the second one. The goal of this article is to further test the accuracy of CombiFF-generated force fields by extending the validation to: (i) nine additional properties that were not used as optimization targets (pure-liquid thermodynamic, dielectric and transport properties, as well as solvation properties); (ii) hetero-polyfunctional molecules that were not included in the calibration and initial validation sets. The results for the nine additional properties show good agreement with experiment, except for the shear viscosity and the dielectric permittivity. There, larger discrepancies are observed, likely due to the united-atom representation adopted for the aliphatic groups and to the implicit treatment of electronic polarization effects. The results for the hetero-polyfunctional molecules also show reasonable agreement with experiment in terms of the monitored properties.
Collapse
Affiliation(s)
- Marina P Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093, Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093, Zürich, Switzerland.
| |
Collapse
|
6
|
Soloviev DO, Hanna FE, Misuraca MC, Hunter CA. H-bond cooperativity: polarisation effects on secondary amides. Chem Sci 2022; 13:11863-11868. [PMID: 36320903 PMCID: PMC9580511 DOI: 10.1039/d2sc04271a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/19/2022] [Indexed: 11/21/2022] Open
Abstract
Formation of a H-bond with an amide carbonyl oxygen atom increases the strength of subsequent H-bonds formed by the amide NH, due to polarisation of the bond. The magnitude of this effect has been quantified by measuring association constants for the formation of 1 : 1 complexes of 2-hydroxylbenzamides with tri-n-butyl phosphine oxide. In 2-hydroxybenzamides, there is an intramolecular H-bond between the phenol OH group and the carbonyl oxygen atom. Comparison of the association constants measured for compounds with and without the 2-hydroxy group allows direct quantification of the effect of the intramolecular H-bond on the H-bond donor properties of the amide NH group. Substituents were used to modulate the strength of the intramolecular and intermolecular H-bonds. The presence of an intramolecular H-bond increases the strength of the intermolecular H-bond by more than one order of magnitude in n-octane solution. The increase in the H-bond donor parameter used to describe the amide NH group is directly proportional to the H-bond donor parameter of the phenol OH group that makes the intramolecular H-bond. These polarisation effects will lead to substantial cooperativity in complex systems that feature networks of non-covalent interactions, and the measurements described here provide a quantitative basis for understanding such phenomena. Formation of an intramolecular phenol-amide H-bond leads to a dramatic increase in the H-bond donor strength of the amide NH group. Polarisation of the amide group is directly proportional to the polarity of the phenol H-bond donor.![]()
Collapse
Affiliation(s)
- Daniil O. Soloviev
- Yusuf Hamied Department of Chemistry, University of CambridgeLensfield RoadCambridge CB2 1EWUK
| | - Fergal E. Hanna
- Yusuf Hamied Department of Chemistry, University of CambridgeLensfield RoadCambridge CB2 1EWUK
| | - Maria Cristina Misuraca
- Yusuf Hamied Department of Chemistry, University of CambridgeLensfield RoadCambridge CB2 1EWUK
| | - Christopher A. Hunter
- Yusuf Hamied Department of Chemistry, University of CambridgeLensfield RoadCambridge CB2 1EWUK
| |
Collapse
|
7
|
Adasme-Carreño F, Alzate-Morales J, Ireta J. Modeling cooperative effects in halogen-bonded infinite linear chains. Phys Chem Chem Phys 2017; 19:18529-18538. [PMID: 28682384 DOI: 10.1039/c7cp03078a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Non-additivity in noncovalent interactions is an important aspect of complex systems that can lead to stronger (cooperative) interactions when three or more molecular units influence each other. The halogen bond (XB) is a highly-directional noncovalent interaction that has been found to be cooperative. Here the strength and nature of cooperativity arising in X-bonded infinite linear chains of cyanogen halides and 4-halopyridines are investigated by means of density functional theory calculations. It is found that cyanogen halide chains are highly cooperative (up to 77%), whereas pyridines are only slightly cooperative (below 21%). It is demonstrated that XB and its non-additivity can be modeled as the sum of a local term, which depends on first nearest-neighbors only, and long-range effective dipole-dipole attractions. It is shown that the local term in cyanogen halides primarily accounts for repulsive short-range screened Coulomb interactions, whereas in 4-halopyridines such a term also includes attractive contributions, which are particularly sizeable in some elongated XB conformations. This outcome reveals differences in the nature of the XBs formed in these molecular systems. Nevertheless, it is shown that both systems behave as effective point dipoles regarding cooperative effects, at any point of the XB dissociation path. As such, these results are useful contributions for the understanding and modeling of non-additive effects of noncovalent interactions.
Collapse
Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente 1141, Casilla 721, Talca, Chile.
| | | | | |
Collapse
|
8
|
Rapid prediction of interaction energies for nucleoside-containing hydrogen-bonded complexes: Lone-pair dipole moment treatment for adenine, cytosine and guanine. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-6295-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
9
|
Horta BAC, Merz PT, Fuchs PFJ, Dolenc J, Riniker S, Hünenberger PH. A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set. J Chem Theory Comput 2016; 12:3825-50. [DOI: 10.1021/acs.jctc.6b00187] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruno A. C. Horta
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Pascal T. Merz
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Patrick F. J. Fuchs
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris-Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Jozica Dolenc
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Chemistry,
Biology and Pharmacy Information Center, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | | |
Collapse
|
10
|
Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| |
Collapse
|
11
|
Fu I, Case DA, Baum J. Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide. Biochemistry 2016; 54:6029-37. [PMID: 26339765 DOI: 10.1021/acs.biochem.5b00622] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In the canonical (G-X-Y)(n) sequence of the fibrillar collagen triple helix, stabilizing direct interchain hydrogen bonding connects neighboring chains. Mutations of G can disrupt these interactions and are linked to connective tissue diseases. Here we integrate computational approaches with nuclear magnetic resonance (NMR) to obtain a dynamic view of hydrogen bonding distributions in the (POG)(4)(-)(POA)-(POG)(5) peptide, showing that the solution conformation, dynamics, and hydrogen bonding deviate from the reported X-ray crystal structure in many aspects. The simulations and NMR data provide clear evidence of inequivalent environments in the three chains. Molecular dynamics (MD) simulations indicate direct interchain hydrogen bonds in the leading chain, water bridges in the middle chain, and nonbridging waters in the trailing chain at the G → A substitution site. Theoretical calculations of NMR chemical shifts using a quantum fragmentation procedure can account for the unusual downfield NMR chemical shifts at the substitution sites and are used to assign the resonances to the individual chains. The NMR and MD data highlight the sensitivity of amide shifts to changes in the acceptor group from peptide carbonyls to water. The results are used to interpret solution NMR data for a variety of glycine substitutions and other sequence triplet interruptions to provide new connections between collagen sequences, their associated structures, dynamical behavior, and their ability to recognize collagen receptors.
Collapse
Affiliation(s)
- Iwen Fu
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University , Piscataway, New Jersey 08854, United States
| | - David A Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Jean Baum
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University , Piscataway, New Jersey 08854, United States
| |
Collapse
|
12
|
Hao JJ, Wang CS. Rapid evaluation of the interaction energies for carbohydrate-containing hydrogen-bonded complexes via the polarizable dipole–dipole interaction model combined with NBO or AM1 charge. RSC Adv 2015. [DOI: 10.1039/c4ra12814a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The polarizable dipole–dipole interaction model has been developed to rapidly and accurately estimate the hydrogen bond distances and interaction energies for carbohydrate-containing hydrogen-bonded complexes.
Collapse
Affiliation(s)
- Jiao-Jiao Hao
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- P. R. China
| | - Chang-Sheng Wang
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- P. R. China
| |
Collapse
|
13
|
Hao J, Li S, Jiang X, Huang C, Wang C. Rapid evaluation of individual hydrogen bonding energies in linear water chains. Chem Res Chin Univ 2014. [DOI: 10.1007/s40242-014-4047-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
14
|
Li SS, Huang CY, Hao JJ, Wang CS. Evaluation of the binding energy for hydrogen-bonded complexes containing amides and peptides. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
15
|
Remya K, Suresh CH. Cooperativity and cluster growth patterns in acetonitrile: A DFT study. J Comput Chem 2014; 35:910-22. [DOI: 10.1002/jcc.23575] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/22/2014] [Accepted: 02/04/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Karunakaran Remya
- Inorganic and Theoretical Chemistry Section, CSTD; CSIR-National Institute for interdisciplinary Science and Technology; Trivandrum 695 019 India
| | - Cherumuttathu H. Suresh
- Inorganic and Theoretical Chemistry Section, CSTD; CSIR-National Institute for interdisciplinary Science and Technology; Trivandrum 695 019 India
| |
Collapse
|
16
|
Sun CL, Ding F, Ding YL, Li Y. The effect of water molecules upon the hydrogen-bonding cooperativity of three-stranded antiparallel β-sheet models. RSC Adv 2014. [DOI: 10.1039/c3ra45892j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
17
|
Li SS, Huang CY, Hao JJ, Wang CS. A polarizable dipole-dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen-bonded complexes. J Comput Chem 2013; 35:415-26. [DOI: 10.1002/jcc.23473] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Shu-Shi Li
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Cui-Ying Huang
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Jiao-Jiao Hao
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Chang-Sheng Wang
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| |
Collapse
|
18
|
Zhu T, Zhang JZH, He X. Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model. J Chem Theory Comput 2013; 9:2104-14. [PMID: 26583557 DOI: 10.1021/ct300999w] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have performed a density functional theory (DFT) calculation of the amide proton NMR chemical shift in proteins using a recently developed automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. Systematic investigation was carried out to examine the influence of explicit solvent molecules, cooperative hydrogen bonding effects, density functionals, size of the basis sets, and the local geometry of proteins on calculated chemical shifts. Our result demonstrates that the predicted amide proton ((1)HN) NMR chemical shift in explicit solvent shows remarkable improvement over that calculated with the implicit solvation model. The cooperative hydrogen bonding effect is also shown to improve the accuracy of (1)HN chemical shifts. Furthermore, we found that the OPBE exchange-correlation functional is the best density functional for the prediction of protein (1)HN chemical shifts among a selective set of DFT methods (namely, B3LYP, B3PW91, M062X, M06L, mPW1PW91, OB98, OPBE), and the locally dense basis set of 6-311++G**/4-31G* is shown to be sufficient for (1)HN chemical shift calculation. By taking ensemble averaging into account, (1)HN chemical shifts calculated by the AF-QM/MM approach can be used to validate the performance of various force fields. Our study underscores that the electronic polarization of protein is of critical importance to stabilizing hydrogen bonding, and the AF-QM/MM method is able to describe the local chemical environment in proteins more accurately than most widely used empirical models.
Collapse
Affiliation(s)
- Tong Zhu
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China 200062
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China 200062.,Department of Chemistry, New York University, New York, New York 10003, United States
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China 200062
| |
Collapse
|
19
|
Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 731] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
| | | |
Collapse
|
20
|
Rapid and accurate evaluation of the binding energies and the individual N-H···O=C, N-H···N, C-H···O=C, and C-H···N interaction energies for hydrogen-bonded peptide-base complexes. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4715-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
21
|
Horta BAC, Lin Z, Huang W, Riniker S, van Gunsteren WF, Hünenberger PH. Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol. J Comput Chem 2012; 33:1907-17. [DOI: 10.1002/jcc.23021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/10/2012] [Accepted: 04/19/2012] [Indexed: 11/09/2022]
|
22
|
Piatkowski L, Bakker HJ. Vibrational relaxation pathways of amide I and amide II modes in N-methylacetamide. J Chem Phys 2012; 136:164504. [DOI: 10.1063/1.4705120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
23
|
Li Y, Wang C. Rapid evaluation of the binding energies between peptide amide and DNA base. J Comput Chem 2011; 32:2765-73. [DOI: 10.1002/jcc.21856] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 04/03/2011] [Accepted: 05/13/2011] [Indexed: 01/22/2023]
Affiliation(s)
- Yang Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Chang‐Sheng Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| |
Collapse
|
24
|
Li Y, Jiang XN, Wang CS. Rapid evaluation of the binding energies in hydrogen-bonded amide-thymine and amide-uracil dimers in gas phase. J Comput Chem 2011; 32:953-66. [PMID: 20949514 DOI: 10.1002/jcc.21680] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Accepted: 08/18/2010] [Indexed: 11/11/2022]
Abstract
The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 48 hydrogen-bonded amide-thymine and amide-uracil dimers are evaluated from the analytic potential energy function established in our lab recently. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6-311+G** calculations by including the BSSE correction. For all the 48 dimers, the analytic potential energy function yields the binding energies of the MP2/6-311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 46 dimers, only two differences are larger than 0.50 kcal/mol and the largest one is only 0.60 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6-311+G** with BSSE correction within the error limits of 0.050 Å for all the 48 dimers. The analytic potential energy function is further applied to four more complicated hydrogen-bonded amide-base systems involving amino acid side chain and β-sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen-bonded amide-base dimers quickly and accurately.
Collapse
Affiliation(s)
- Yang Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | | | | |
Collapse
|
25
|
Mahadevi AS, Neela YI, Sastry GN. A theoretical study on structural, spectroscopic and energetic properties of acetamide clusters [CH3CONH2] (n = 1–15). Phys Chem Chem Phys 2011; 13:15211-20. [DOI: 10.1039/c1cp21346f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
26
|
Piatkowski L, Bakker HJ. Vibrational Relaxation Pathways of AI and AII Modes in N-Methylacetamide Clusters. J Phys Chem A 2010; 114:11462-70. [DOI: 10.1021/jp107590b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- L. Piatkowski
- FOM Istitute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - H. J. Bakker
- FOM Istitute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
| |
Collapse
|
27
|
Sun CL, Wang CS. Estimation on the intramolecular hydrogen-bonding energies in proteins and peptides by the analytic potential energy function. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.06.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|